3NS4 | pdb_00003ns4

Structure of a C-terminal fragment of its Vps53 subunit suggests similarity of GARP to a family of tethering complexes


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529550 mM Tris at pH 8.5, 10% PEG 4K, 200 mM BaCl2, and 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.9958.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.236α = 90
b = 127.236β = 90
c = 81.658γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113CCDADSC QUANTUM 3152009-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97915APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.92510086088606
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.93100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.924.48608860642899.980.191140.189630.20.220720.22RANDOM61.519
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.69-0.34-0.691.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.343
r_scangle_it12.297
r_dihedral_angle_3_deg11.828
r_dihedral_angle_4_deg10.535
r_scbond_it7.733
r_mcangle_it4.52
r_dihedral_angle_1_deg3.206
r_mcbond_it1.86
r_angle_refined_deg1.768
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.343
r_scangle_it12.297
r_dihedral_angle_3_deg11.828
r_dihedral_angle_4_deg10.535
r_scbond_it7.733
r_mcangle_it4.52
r_dihedral_angle_1_deg3.206
r_mcbond_it1.86
r_angle_refined_deg1.768
r_chiral_restr0.115
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1711
Nucleic Acid Atoms
Solvent Atoms19
Heterogen Atoms3

Software

Software
Software NamePurpose
HKL-2000data collection
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling